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- PDB-6t14: Native structure of mosquitocidal Cyt1A protoxin obtained by Seri... -

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Basic information

Entry
Database: PDB / ID: 6t14
TitleNative structure of mosquitocidal Cyt1A protoxin obtained by Serial Femtosecond Crystallography on in vivo grown crystals at pH 7
ComponentsType-1Aa cytolytic delta-endotoxin
KeywordsTOXIN / Mosquitocidal toxin / in vivo grown nanocrystals
Function / homologyDelta-endotoxin CytB / Delta-endotoxin CytB-like superfamily / Bacillus thuringiensis toxin / sporulation resulting in formation of a cellular spore / toxin activity / extracellular region / Type-1Aa cytolytic delta-endotoxin
Function and homology information
Biological speciesBacillus thuringiensis subsp. israelensis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsTetreau, G. / Banneville, A.S. / Andreeva, E. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Young, I.D. / Boutet, S. / Coquelle, N. / Cascio, D. ...Tetreau, G. / Banneville, A.S. / Andreeva, E. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Young, I.D. / Boutet, S. / Coquelle, N. / Cascio, D. / Sawaya, M.R. / Sauter, N.K. / Colletier, J.P.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE11-0018-01 France
French National Research AgencyANR-2018-CE11-0005-02 France
CitationJournal: Nat Commun / Year: 2020
Title: Serial femtosecond crystallography on in vivo-grown crystals drives elucidation of mosquitocidal Cyt1Aa bioactivation cascade.
Authors: Tetreau, G. / Banneville, A.S. / Andreeva, E.A. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Teulon, J.M. / Young, I.D. / Burke, N. / Grunewald, T.A. / Beaudouin, J. / Snigireva, I. / ...Authors: Tetreau, G. / Banneville, A.S. / Andreeva, E.A. / Brewster, A.S. / Hunter, M.S. / Sierra, R.G. / Teulon, J.M. / Young, I.D. / Burke, N. / Grunewald, T.A. / Beaudouin, J. / Snigireva, I. / Fernandez-Luna, M.T. / Burt, A. / Park, H.W. / Signor, L. / Bafna, J.A. / Sadir, R. / Fenel, D. / Boeri-Erba, E. / Bacia, M. / Zala, N. / Laporte, F. / Despres, L. / Weik, M. / Boutet, S. / Rosenthal, M. / Coquelle, N. / Burghammer, M. / Cascio, D. / Sawaya, M.R. / Winterhalter, M. / Gratton, E. / Gutsche, I. / Federici, B. / Pellequer, J.L. / Sauter, N.K. / Colletier, J.P.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
BBB: Type-1Aa cytolytic delta-endotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3782
Polymers27,3551
Non-polymers231
Water4,414245
1
BBB: Type-1Aa cytolytic delta-endotoxin
hetero molecules

BBB: Type-1Aa cytolytic delta-endotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7564
Polymers54,7102
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area6540 Å2
ΔGint-49 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.781, 64.781, 164.482
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11BBB-618-

HOH

21BBB-644-

HOH

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Components

#1: Protein Type-1Aa cytolytic delta-endotoxin / 27 kDa cytolytic toxin


Mass: 27354.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: nanocrystals were grown in vivo
Source: (gene. exp.) Bacillus thuringiensis subsp. israelensis (bacteria)
Gene: cyt1Aa, cytA
Production host: Bacillus thuringiensis serovar israelensis (bacteria)
Variant (production host): 4Q7 / References: UniProt: P0A382
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.91 % / Description: Bipyramidal crystals
Crystal growTemperature: 300 K / Method: in cell
Details: In cell crystallization by recombinant expression in a Bacillus thuringiensis serovar israelensis strain devoid of its pBt plasmid.

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Data collection

DiffractionMean temperature: 300 K / Ambient temp details: data collection in a vacuum chamber / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.28 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Nov 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 17966 / % possible obs: 98.7 % / Redundancy: 107.8 % / CC1/2: 0.995 / R split: 0.125 / Net I/σ(I): 18.6
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 17.96 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 898 / CC1/2: 0.078 / R split: 0.877 / % possible all: 100
Serial crystallography measurementFocal spot size: 1.7 µm2 / Pulse duration: 40 fsec. / Pulse energy: 1000 µJ / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionDescription: MESH
Serial crystallography data reductionFrames indexed: 8462 / Frames total: 65473 / Lattices indexed: 8584

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Processing

Software
NameVersionClassification
REFMAC5.8.0230 2018/03/05refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ron

3ron


Resolution: 1.86→26.549 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.161 / WRfactor Rwork: 0.145 / Cross valid method: FREE R-VALUE / ESU R: 0.227 / ESU R Free: 0.181
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2559 845 -
Rwork0.2179 16099 -
all0.22 --
obs-16944 94.254 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 29.343 Å2
Baniso -1Baniso -2Baniso -3
1--0.014 Å2-0.007 Å20 Å2
2---0.014 Å20 Å2
3---0.047 Å2
Refinement stepCycle: LAST / Resolution: 1.86→26.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 1 245 2128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0141962
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171783
X-RAY DIFFRACTIONr_angle_refined_deg0.8841.6472692
X-RAY DIFFRACTIONr_angle_other_deg1.4041.6264171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2525253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.22826.29289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58115323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.074153
X-RAY DIFFRACTIONr_chiral_restr0.0710.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022213
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02343
X-RAY DIFFRACTIONr_nbd_refined0.1990.2353
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.21642
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2929
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2894
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2151
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.230
X-RAY DIFFRACTIONr_nbd_other0.1860.2136
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.277
X-RAY DIFFRACTIONr_mcbond_it0.9452.8821000
X-RAY DIFFRACTIONr_mcbond_other0.9442.881999
X-RAY DIFFRACTIONr_mcangle_it1.6164.3181257
X-RAY DIFFRACTIONr_mcangle_other1.6164.3191258
X-RAY DIFFRACTIONr_scbond_it1.042.967960
X-RAY DIFFRACTIONr_scbond_other1.0392.967960
X-RAY DIFFRACTIONr_scangle_it1.7094.4181435
X-RAY DIFFRACTIONr_scangle_other1.7094.4181435
X-RAY DIFFRACTIONr_lrange_it5.0835.2552156
X-RAY DIFFRACTIONr_lrange_other4.25934.1522092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.86-1.9080.452590.4991126129391.64730.489
1.908-1.960.459570.4371043124588.35340.423
1.96-2.0170.43560.3781067122891.44950.36
2.017-2.0780.351510.3451049118492.90540.314
2.078-2.1460.34550.3071006115392.02080.279
2.146-2.2210.279510.264972111391.91370.23
2.221-2.3040.331510.241966108793.56030.207
2.304-2.3970.311490.229934105193.530.191
2.397-2.5030.287480.225897100294.31140.186
2.503-2.6240.225440.22387196494.9170.186
2.624-2.7640.317440.21984992596.54050.179
2.764-2.930.318450.20381188396.94220.159
2.93-3.130.257390.19175882896.2560.15
3.13-3.3770.199370.1771678096.53850.132
3.377-3.6930.187370.14167772598.48280.11
3.693-4.1190.214330.14963567299.40480.117
4.119-4.7370.188280.13956459898.99670.108
4.737-5.7560.153240.1648752098.26920.126
5.756-7.9560.241220.20840542899.76640.168
7.956-26.5490.124150.17126628598.59650.137

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